--------------------------------------------------------------------------------
|             Helix Systems -- Center for Information Technology               |
|                            http://helix.nih.gov                              |
|   National Institutes of Health, Department of Health and Human Services     |
|                                                                              |
|             DNAWorks Web Site: http://helixweb.nih.gov/dnaworks              |
--------------------------------------------------------------------------------
|                                                                              |
|              Send all correspondence to webtools@helix.nih.gov               |
--------------------------------------------------------------------------------

 Job started on 06/17/2011 at 14:46:29

 Job name: IS6172011ShigellaflexneriApyrase                                     

 Output will be sent to indyshukla92@gmail.com        
 
      SEQUENCE  1: PROTEIN LENGTH =  247                               
 ----------------------------------------------------------------
   1 MKTKNFLLFCIATNMIFIPSANALKAEGFLTQQTSPDSLSILPPPPAEDSVVFLADKAHY
  61 EFGRSLRDANRVRLASEDAYYENFGLAFSDAYGMDISRENTPILYQLLTQVLQDSHDYAV
 121 RNAKEYYKRVRPFVIYKDATCTPDKDEKMAITGSYPSGHASFGWAVALILAEINPQRKAE
 181 ILRRGYEFGESRVICGAHWQSDVEAGRLMGASVVAVLHNTPEFTKSLSEAKKEFEELNTP
 241 TNELTPX
 ----------------------------------------------------------------
 
             CODON FREQUENCY TABLE: E. coli Class II              
 ----------------------------------------------------------------
 
      TTT F 0.291   TCT S 0.324   TAT Y 0.352   TGT C 0.389
      TTC F 0.709   TCC S 0.266   TAC Y 0.648   TGC C 0.612
      TTA L 0.034   TCA S 0.048   TAA X 0.630   TGA X 0.352
      TTG L 0.055   TCG S 0.074   TAG X 0.076   TGG W 1.000
 
      CTT L 0.056   CCT P 0.112   CAT H 0.298   CGT R 0.643
      CTC L 0.080   CCC P 0.016   CAC H 0.702   CGC R 0.330
      CTA L 0.008   CCA P 0.153   CAA Q 0.187   CGA R 0.011
      CTG L 0.767   CCG P 0.719   CAG Q 0.814   CGG R 0.008
 
      ATT I 0.335   ACT T 0.291   AAT N 0.173   AGT S 0.045
      ATC I 0.659   ACC T 0.536   AAC N 0.828   AGC S 0.243
      ATA I 0.006   ACA T 0.047   AAA K 0.786   AGA R 0.006
      ATG M 1.000   ACG T 0.127   AAG K 0.215   AGG R 0.003
 
      GTT V 0.398   GCT A 0.275   GAT D 0.461   GGT G 0.508
      GTC V 0.135   GCC A 0.161   GAC D 0.540   GGC G 0.428
      GTA V 0.200   GCA A 0.240   GAA E 0.754   GGA G 0.020
      GTG V 0.268   GCG A 0.323   GAG E 0.247   GGG G 0.044
 
 
             ACTIVE CODONS FOR SEQUENCE GENERATION 
 
  Residue   Codons   Active Codons     Min. Freq.    Max. Freq.
 ----------------------------------------------------------------
   A  Ala      4           4             0.161         0.323
   C  Cys      2           2             0.389         0.612
   D  Asp      2           2             0.461         0.540
 
   E  Glu      2           2             0.247         0.754
   F  Phe      2           2             0.291         0.709
   G  Gly      4           2             0.428         0.508
 
   H  His      2           2             0.298         0.702
   I  Ile      3           2             0.335         0.659
   K  Lys      2           2             0.215         0.786
 
   L  Leu      6           2             0.080         0.767
   M  Met      1           1             1.000         1.000
   N  Asn      2           2             0.173         0.828
 
   P  Pro      4           3             0.112         0.719
   Q  Gln      2           2             0.187         0.814
   R  Arg      6           2             0.330         0.643
 
   S  Ser      6           3             0.243         0.324
   T  Thr      4           3             0.127         0.536
   V  Val      4           4             0.135         0.398
 
   W  Trp      1           1             1.000         1.000
   X  End      3           2             0.352         0.630
   Y  Tyr      2           2             0.352         0.648
 
 
                SEQUENCE PATTERNS TO BE SCREENED
 ----------------------------------------------------------------
 ----------------------------------------------------------------
 
 ----------------------------------------------------------------
                    PARAMETERS FOR TRIAL 1                             
 ----------------------------------------------------------------
               Total Size Of Gene ......... 741 nt                        
               Protein Residues ........... 247                           
               Mutatable Residues ......... 240                           
               Fixed Nucleotides .......... 21 nt                         
               Oligo Size ................. 60 nt                         
               Annealing Temp ............. 62 +/- 1*C                    
               Oligo Concentration ........ 1.00E-7 M                     
               Sodium Concentration ....... 5.00E-2 M                     
               Mg2+ Concentration ......... 2.00E-3 M                     
               Codon Frequency Threshold .. 10%                           
               Repeat Threshold ........... 8 nt                          
               Mispriming Threshold ....... 8/18 (6 exact) nt             
 
--------------------------------------------------------------------------------
 
 The DNA sequence #   1 is:
 ----------------------------------------------------------------
   1 ATGAAAACCAAAAACTTCCTGCTGTTTTGCATTGCGACCAATATGATCTTCATCCCGTCT
  61 GCGAACGCCCTGAAAGCAGAAGGTTTCCTCACCCAGCAGACCTCTCCGGATTCTCTGTCT
 121 ATCCTGCCGCCACCGCCAGCGGAGGATTCTGTTGTTTTCCTGGCGGACAAAGCGCACTAC
 181 GAATTTGGTCGTTCTCTCCGTGACGCGAACCGCGTTCGTCTGGCGTCTGAAGATGCGTAC
 241 TACGAGAACTTCGGTCTCGCCTTCTCTGACGCGTACGGTATGGACATCTCTCGTGAAAAC
 301 ACCCCGATCCTGTACCAGCTGCTGACCCAGGTACTGCAGGACTCTCATGACTATGCTGTT
 361 CGCAACGCTAAAGAATACTACAAACGTGTTCGCCCGTTCGTTATCTACAAAGACGCGACC
 421 TGCACCCCGGATAAAGACGAAAAAATGGCGATCACCGGTTCTTACCCGTCCGGTCACGCG
 481 AGCTTCGGTTGGGCGGTTGCGCTGATCCTGGCAGAAATCAACCCGCAGCGTAAAGCGGAA
 541 ATCCTGCGTCGTGGTTACGAGTTCGGTGAATCTCGTGTTATCTGCGGCGCACACTGGCAG
 601 TCCGACGTTGAAGCGGGTCGTCTGATGGGTGCGTCTGTAGTTGCGGTGCTGCACAACACG
 661 CCGGAATTCACCAAATCTCTGAGCGAAGCGAAGAAAGAATTCGAAGAACTGAACACTCCG
 721 ACCAACGAACTGACCCCGTAA
 ----------------------------------------------------------------
 
 The oligonucleotide assembly is:
 ----------------------------------------------------------------
     1       10        20        30        40        50        60
     |        |         |         |         |         |         |
 
     1 --->                                                      
   1 ATGAAAACCAAAAACTTCCTGCTGTTTTGCATTGCGACCAATATGATCTTCATCC     
                                      CGCTGGTTATACTAGAAGTAGGGCAGA
                                                                 
      M  K  T  K  N  F  L  L  F  C  I  A  T  N  M  I  F  I  P  S 
 
     |        |         |         |         |         |         |
 
                 3 --->                                          
  61             aaagcagaaggtttcctcacccagcagacctctccggattctctgtct
     CGCTTGCGGGACTTTCGTCTTCCAAAGGAGTGG                     gacaga
                               <---  2                           
      A  N  A  L  K  A  E  G  F  L  T  Q  Q  T  S  P  D  S  L  S 
 
     |        |         |         |         |         |         |
 
                                           5 --->                
 121 atcctgccgcca                          CCTGGCGGACAAAGCGCACTAC
     taggacggcggtggcggtcgcctcctaagacaacaaaaggaccgcctgtttcgc      
                                                    <---  4      
      I  L  P  P  P  P  A  E  D  S  V  V  F  L  A  D  K  A  H  Y 
 
     |        |         |         |         |         |         |
 
                                                                 
 181 GAATTTGGTCGTTCTCTCCGTGACGCGAACCGCGTTCG                      
                            GCGCTTGGCGCAAGCAGACCGCAGACTTCTACGCATG
                                                                 
      E  F  G  R  S  L  R  D  A  N  R  V  R  L  A  S  E  D  A  Y 
 
     |        |         |         |         |         |         |
 
         7 --->                                                  
 241     agaacttcggtctcgccttctctgacgcgtacggtatggacatctctcgtgaaaac
     ATGCTCTTGAAGCCAGAGCGGAA                    tgtagagagcacttttg
                     <---  6                                     
      Y  E  N  F  G  L  A  F  S  D  A  Y  G  M  D  I  S  R  E  N 
 
     |        |         |         |         |         |         |
 
                              9 --->                             
 301 accc                     CCCAGGTACTGCAGGACTCTCATGACTATGCTGTT
     tggggctaggacatggtcgacgactgggtccatgacgtcctga                 
                                         <---  8                 
      T  P  I  L  Y  Q  L  L  T  Q  V  L  Q  D  S  H  D  Y  A  V 
 
     |        |         |         |         |         |         |
 
                                             11 --->             
 361 CGCAACGCTAAAGAATACTACAAAC               ttatctacaaagacgcgacc
      CGTTGCGATTTCTTATGATGTTTGCACAAGCGGGCAAGCAATAGATGTTTCTGCGCTGG
                                                           <--- 1
      R  N  A  K  E  Y  Y  K  R  V  R  P  F  V  I  Y  K  D  A  T 
 
     |        |         |         |         |         |         |
 
                                                                 
 421 tgcaccccggataaagacgaaaaaatggcgatcaccggtt                    
     A                    ttttaccgctagtggccaagaatgggcaggccagtgcgc
     0                                                           
      C  T  P  D  K  D  E  K  M  A  I  T  G  S  Y  P  S  G  H  A 
 
     |        |         |         |         |         |         |
 
           13 --->                                               
 481       GGTTGGGCGGTTGCGCTGATCCTGGCAGAAATCAACCCGCAGCGTAAAGCGGAA
     tcgaagccaacccgccaacgc                         TCGCATTTCGCCTT
                   <--- 12                                       
      S  F  G  W  A  V  A  L  I  L  A  E  I  N  P  Q  R  K  A  E 
 
     |        |         |         |         |         |         |
 
                              15 --->                            
 541 ATCCTG                   gtgaatctcgtgttatctgcggcgcacactggcag
     TAGGACGCAGCACCAATGCTCAAGCCACTTAGAGCACAATAGACGC              
                                            <--- 14              
      I  L  R  R  G  Y  E  F  G  E  S  R  V  I  C  G  A  H  W  Q 
 
     |        |         |         |         |         |         |
 
                                                       17 --->   
 601 tccgacgttgaagcgggtcgtctga                         GCACAACACG
             acttcgcccagcagactacccacgcagacatcaacgccacgacgtgttgtgc
                                                                 
      S  D  V  E  A  G  R  L  M  G  A  S  V  V  A  V  L  H  N  T 
 
     |        |         |         |         |         |         |
 
                                                                 
 661 CCGGAATTCACCAAATCTCTGAGCGAAGCGAAGAAAGAATTCGAAGAACT          
     ggccttaa                   CGCTTCTTTCTTAAGCTTCTTGACTTGTGAGGC
      <--- 16                                                    
      P  E  F  T  K  S  L  S  E  A  K  K  E  F  E  E  L  N  T  P 
 
     |        |         |         |         |         |         |
 
                          
 721                      
     TGGTTGCTTGACTGGGGCATT
                   <--- 18
      T  N  E  L  T  P  X 
 ----------------------------------------------------------------
 
 The total codon usage score ...........     0.000
 The total length score ................     0.000
 The total melting temperature score ...     0.000
 The total repeat score ................     0.000
 The total pattern score ...............     0.000
 The total mispriming score ............     0.000
 The total AT content score ............     0.000
 The total GC content score ............     0.000
 The total fixed gap score .............      N/A
                The OVERALL score ......     0.000
 
 
                  DETAILED CODON FREQUENCY REPORT 
  [ Codon, AA, Frequency, # of times used in coding sequence ] 
 ----------------------------------------------------------------
 
 TTT F 0.29   2  TCT S 0.32  14  TAT Y 0.35   1  TGT C 0.39   0
 TTC F 0.71  11  TCC S 0.27   2  TAC Y 0.65  10  TGC C 0.61   3
 TTA L 0.03   0  TCA S 0.05   0  TAA X 0.63   1  TGA X 0.35   0
 TTG L 0.06   0  TCG S 0.07   0  TAG X 0.08   0  TGG W 1.00   2
 
 CTT L 0.06   0  CCT P 0.11   0  CAT H 0.30   1  CGT R 0.64  10
 CTC L 0.08   3  CCC P 0.02   0  CAC H 0.70   4  CGC R 0.33   3
 CTA L 0.01   0  CCA P 0.15   2  CAA Q 0.19   0  CGA R 0.01   0
 CTG L 0.77  19  CCG P 0.72  12  CAG Q 0.81   7  CGG R 0.01   0
 
 ATT I 0.34   1  ACT T 0.29   1  AAT N 0.17   1  AGT S 0.05   0
 ATC I 0.66  11  ACC T 0.54  12  AAC N 0.83  10  AGC S 0.24   2
 ATA I 0.01   0  ACA T 0.05   0  AAA K 0.79  12  AGA R 0.01   0
 ATG M 1.00   5  ACG T 0.13   1  AAG K 0.22   1  AGG R 0.00   0
 
 GTT V 0.40  10  GCT A 0.28   2  GAT D 0.46   4  GGT G 0.51  11
 GTC V 0.14   0  GCC A 0.16   2  GAC D 0.54   9  GGC G 0.43   1
 GTA V 0.20   2  GCA A 0.24   3  GAA E 0.75  16  GGA G 0.02   0
 GTG V 0.27   1  GCG A 0.32  19  GAG E 0.25   3  GGG G 0.04   0
 
             
              Frequency Range   Number of Codons
             -------------------------------------
                0% -  4%                  0
                5% -  9%                  3
               10% - 14%                  1
               15% - 19%                  5
               20% - 24%                 11
               25% - 29%                  9
               30% - 34%                 37
               35% - 39%                 11
               40% - 44%                  1
               45% - 49%                  4
                  >= 50%                165
             -------------------------------------
              Total Codons Used =   247
 
                  Tm Range    # of Overlaps 
             -------------------------------------
                   <59            0
                    59            0
                    60            0
                    61            9
                    62            8
                    63            0
                    64            0
                    65            0
                    66            0
                  >=67            0
             -------------------------------------
              Tm Range =  1.9
 
              Ovrlap Len Range  # of Oligos
             -------------------------------------
                   <16            2
                    16            1
                    17            1
                    18            3
                    19            2
                    20            1
                    21            4
                    22            1
                    23            1
                    24            1
                    25            0
                  >=26            0
             -------------------------------------
              Lowest Overlap = 15
 
              Length Range   # of Oligos
             -------------------------------------
                   <51            0
                  51-52           0
                  53-54           1
                  55-56           1
                  57-58           0
                  59-60          16
                  61-62           0
                  63-64           0
                  65-66           0
                  67-68           0
                  69-70           0
                   >=71           0
             -------------------------------------
              Longest =  60
 
 
          Sequence Patterns Screened (As Supplied By User)
 ----------------------------------------------------------------
                       None found
 ----------------------------------------------------------------
 
        18 oligonucleotides need to be synthesized
 ----------------------------------------------------------------
  1 ATGAAAACCAAAAACTTCCTGCTGTTTTGCATTGCGACCAATATGATCTTCATCC  55
  2 GGTGAGGAAACCTTCTGCTTTCAGGGCGTTCGCAGACGGGATGAAGATCATATTGGTCGC  60
  3 AAAGCAGAAGGTTTCCTCACCCAGCAGACCTCTCCGGATTCTCTGTCTATCCTGCCGCCA  60
  4 CGCTTTGTCCGCCAGGAAAACAACAGAATCCTCCGCTGGCGGTGGCGGCAGGATAGACAG  60
  5 CCTGGCGGACAAAGCGCACTACGAATTTGGTCGTTCTCTCCGTGACGCGAACCGCGTTCG  60
  6 AAGGCGAGACCGAAGTTCTCGTAGTACGCATCTTCAGACGCCAGACGAACGCGGTTCGCG  60
  7 AGAACTTCGGTCTCGCCTTCTCTGACGCGTACGGTATGGACATCTCTCGTGAAAACACCC  60
  8 AGTCCTGCAGTACCTGGGTCAGCAGCTGGTACAGGATCGGGGTGTTTTCACGAGAGATGT  60
  9 CCCAGGTACTGCAGGACTCTCATGACTATGCTGTTCGCAACGCTAAAGAATACTACAAAC  60
 10 AGGTCGCGTCTTTGTAGATAACGAACGGGCGAACACGTTTGTAGTATTCTTTAGCGTTGC  60
 11 TTATCTACAAAGACGCGACCTGCACCCCGGATAAAGACGAAAAAATGGCGATCACCGGTT  60
 12 CGCAACCGCCCAACCGAAGCTCGCGTGACCGGACGGGTAAGAACCGGTGATCGCCATTTT  60
 13 GGTTGGGCGGTTGCGCTGATCCTGGCAGAAATCAACCCGCAGCGTAAAGCGGAAATCCTG  60
 14 CGCAGATAACACGAGATTCACCGAACTCGTAACCACGACGCAGGATTTCCGCTTTACGCT  60
 15 GTGAATCTCGTGTTATCTGCGGCGCACACTGGCAGTCCGACGTTGAAGCGGGTCGTCTGA  60
 16 AATTCCGGCGTGTTGTGCAGCACCGCAACTACAGACGCACCCATCAGACGACCCGCTTCA  60
 17 GCACAACACGCCGGAATTCACCAAATCTCTGAGCGAAGCGAAGAAAGAATTCGAAGAACT  60
 18 TTACGGGGTCAGTTCGTTGGTCGGAGTGTTCAGTTCTTCGAATTCTTTCTTCGC  54
 
                          FINAL SUMMARY FOR   1 SOLUTION   
--------------------------------------------------------------------------------
  #    Tm   Len  |    Score   TmRange  Short    Long   #Olig  #Repeat #Misprime
 
  1    62    60  |    0.000       1.9      15      60      18       0       0
 
--------------------------------------------------------------------------------
|             Helix Systems -- Center for Information Technology               |
|                            http://helix.nih.gov                              |
|   National Institutes of Health, Department of Health and Human Services     |
|                                                                              |
|             DNAWorks Web Site: http://helixweb.nih.gov/dnaworks              |
--------------------------------------------------------------------------------

